Chosen Solution
Initially the fault was determined to be the U2 Tristar Charging IC chip (or whatever it’s called on iPhone 5s). So I got it replaced but I still have the issue of it not charging the battery. Tried another battery, might think of trying another charging port later. But what it does now it can still turn on, every thing works fine (excluding the fingerprint scanner since it got replaced) also the battery does work but does not get charged. Tried two batteries already, charge not going to the battery. Is there some capacitor that I should check if it needs replacing on the charging circuit? TL-DR: It’s basically detecting plugged in on charging but not charging. Update (09/12/2016) Thanks for the advice @oldturkey03! Changing the charger port allowed the battery to start getting power from the charging cable.
Marking as solved so I don’t get emails of it not being solved.